py-cutadapt: Resurrect and update to 4.6

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Feb 4 09:44:49 2024 -0600
Changeset:	87ebf0b4184304c548435bf22c3ecd6220d36d92

Added Files:
	py-cutadapt/DESCR
	py-cutadapt/Makefile
	py-cutadapt/PLIST
	py-cutadapt/distinfo

Log Message:
py-cutadapt: Resurrect and update to 4.6

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=87ebf0b4184304c548435bf22c3ecd6220d36d92

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 py-cutadapt/DESCR    |  2 ++
 py-cutadapt/Makefile | 19 +++++++++++++
 py-cutadapt/PLIST    | 79 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 py-cutadapt/distinfo |  5 ++++
 4 files changed, 105 insertions(+)

diffs:
diff --git a/py-cutadapt/DESCR b/py-cutadapt/DESCR
new file mode 100644
index 0000000000..0adbe298ed
--- /dev/null
+++ b/py-cutadapt/DESCR
@@ -0,0 +1,2 @@
+Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
+types of unwanted sequence from your high-throughput sequencing reads.
diff --git a/py-cutadapt/Makefile b/py-cutadapt/Makefile
new file mode 100644
index 0000000000..bb6ec12b34
--- /dev/null
+++ b/py-cutadapt/Makefile
@@ -0,0 +1,19 @@
+# $NetBSD$
+
+DISTNAME=	cutadapt-4.6
+PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_PYPI:=c/cutadapt/}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://cutadapt.readthedocs.io/en/stable/
+COMMENT=	Find and remove adapter sequences, primers, poly-A tails, etc
+LICENSE=	mit
+
+DEPENDS+=	${PYPKGPREFIX}-xopen>=1.0.0:../../devel/py-xopen
+DEPENDS+=	${PYPKGPREFIX}-dnaio>=0.5.0:../../wip/py-dnaio
+
+PYTHON_SELF_CONFLICT=	yes
+
+.include "../../lang/python/wheel.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-cutadapt/PLIST b/py-cutadapt/PLIST
new file mode 100644
index 0000000000..deb85e0075
--- /dev/null
+++ b/py-cutadapt/PLIST
@@ -0,0 +1,79 @@
+@comment $NetBSD$
+bin/cutadapt
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/entry_points.txt
+${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
+${PYSITELIB}/cutadapt/__init__.py
+${PYSITELIB}/cutadapt/__init__.pyc
+${PYSITELIB}/cutadapt/__init__.pyo
+${PYSITELIB}/cutadapt/__main__.py
+${PYSITELIB}/cutadapt/__main__.pyc
+${PYSITELIB}/cutadapt/__main__.pyo
+${PYSITELIB}/cutadapt/_align.pyi
+${PYSITELIB}/cutadapt/_align.so
+${PYSITELIB}/cutadapt/_kmer_finder.pyi
+${PYSITELIB}/cutadapt/_kmer_finder.so
+${PYSITELIB}/cutadapt/_match_tables.py
+${PYSITELIB}/cutadapt/_match_tables.pyc
+${PYSITELIB}/cutadapt/_match_tables.pyo
+${PYSITELIB}/cutadapt/_version.py
+${PYSITELIB}/cutadapt/_version.pyc
+${PYSITELIB}/cutadapt/_version.pyo
+${PYSITELIB}/cutadapt/adapters.py
+${PYSITELIB}/cutadapt/adapters.pyc
+${PYSITELIB}/cutadapt/adapters.pyo
+${PYSITELIB}/cutadapt/align.py
+${PYSITELIB}/cutadapt/align.pyc
+${PYSITELIB}/cutadapt/align.pyo
+${PYSITELIB}/cutadapt/cli.py
+${PYSITELIB}/cutadapt/cli.pyc
+${PYSITELIB}/cutadapt/cli.pyo
+${PYSITELIB}/cutadapt/files.py
+${PYSITELIB}/cutadapt/files.pyc
+${PYSITELIB}/cutadapt/files.pyo
+${PYSITELIB}/cutadapt/info.pyi
+${PYSITELIB}/cutadapt/info.so
+${PYSITELIB}/cutadapt/json.py
+${PYSITELIB}/cutadapt/json.pyc
+${PYSITELIB}/cutadapt/json.pyo
+${PYSITELIB}/cutadapt/kmer_heuristic.py
+${PYSITELIB}/cutadapt/kmer_heuristic.pyc
+${PYSITELIB}/cutadapt/kmer_heuristic.pyo
+${PYSITELIB}/cutadapt/log.py
+${PYSITELIB}/cutadapt/log.pyc
+${PYSITELIB}/cutadapt/log.pyo
+${PYSITELIB}/cutadapt/modifiers.py
+${PYSITELIB}/cutadapt/modifiers.pyc
+${PYSITELIB}/cutadapt/modifiers.pyo
+${PYSITELIB}/cutadapt/parser.py
+${PYSITELIB}/cutadapt/parser.pyc
+${PYSITELIB}/cutadapt/parser.pyo
+${PYSITELIB}/cutadapt/pipeline.py
+${PYSITELIB}/cutadapt/pipeline.pyc
+${PYSITELIB}/cutadapt/pipeline.pyo
+${PYSITELIB}/cutadapt/predicates.py
+${PYSITELIB}/cutadapt/predicates.pyc
+${PYSITELIB}/cutadapt/predicates.pyo
+${PYSITELIB}/cutadapt/qualtrim.pyi
+${PYSITELIB}/cutadapt/qualtrim.so
+${PYSITELIB}/cutadapt/report.py
+${PYSITELIB}/cutadapt/report.pyc
+${PYSITELIB}/cutadapt/report.pyo
+${PYSITELIB}/cutadapt/runners.py
+${PYSITELIB}/cutadapt/runners.pyc
+${PYSITELIB}/cutadapt/runners.pyo
+${PYSITELIB}/cutadapt/statistics.py
+${PYSITELIB}/cutadapt/statistics.pyc
+${PYSITELIB}/cutadapt/statistics.pyo
+${PYSITELIB}/cutadapt/steps.py
+${PYSITELIB}/cutadapt/steps.pyc
+${PYSITELIB}/cutadapt/steps.pyo
+${PYSITELIB}/cutadapt/tokenizer.py
+${PYSITELIB}/cutadapt/tokenizer.pyc
+${PYSITELIB}/cutadapt/tokenizer.pyo
+${PYSITELIB}/cutadapt/utils.py
+${PYSITELIB}/cutadapt/utils.pyc
+${PYSITELIB}/cutadapt/utils.pyo
diff --git a/py-cutadapt/distinfo b/py-cutadapt/distinfo
new file mode 100644
index 0000000000..567efdd83e
--- /dev/null
+++ b/py-cutadapt/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+BLAKE2s (cutadapt-4.6.tar.gz) = 5a77d2a4b39e59f207c330cfd74641a228940dea50e36f6673b341ec432f57ec
+SHA512 (cutadapt-4.6.tar.gz) = b7ab31c6df72d970625edbf3dd0d0970a99c1a044b898449ec059d261db6f64b1b756a8a937217fb3f298cf4cb002c4a8c616402ec7dbc28fc2cc16ea05c2faf
+Size (cutadapt-4.6.tar.gz) = 250254 bytes